Variant report

Variant	rs17176439
Chromosome Location	chr8:59043487-59043488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:59041929..59045530-chr8:59049327..59051439,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10504240	1.00[CEU][hapmap]
rs1507080	0.82[CEU][hapmap]
rs1507081	0.82[CEU][hapmap]
rs16923020	0.82[CEU][hapmap]
rs16923023	0.82[CEU][hapmap]
rs16923044	0.82[CEU][hapmap];1.00[GIH][hapmap]
rs16923053	0.82[CEU][hapmap];1.00[GIH][hapmap]
rs16923066	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs16923074	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs16923080	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6471683	0.82[CEU][hapmap]
rs66631237	0.95[EUR][1000 genomes]
rs72662411	0.95[EUR][1000 genomes]
rs72662413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831324	chr8:58844151-59045309	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17176439	NXN	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59011600-59044800	Weak transcription	Spleen	Spleen
2	chr8:59015200-59058200	Weak transcription	Aorta	Aorta
3	chr8:59016600-59046200	Weak transcription	Fetal Brain Male	brain
4	chr8:59021800-59044200	Weak transcription	Fetal Lung	lung
5	chr8:59022400-59050000	Weak transcription	Ovary	ovary
6	chr8:59026000-59050600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:59026200-59049800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:59029000-59058000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr8:59032000-59047200	Weak transcription	Liver	Liver
10	chr8:59032000-59049200	Weak transcription	Brain Hippocampus Middle	brain
11	chr8:59033200-59045800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr8:59033800-59044800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr8:59033800-59046000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:59033800-59050200	Weak transcription	Pancreas	Pancrea
15	chr8:59034800-59054200	Weak transcription	Fetal Brain Female	brain
16	chr8:59035800-59044800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:59036000-59044600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:59036200-59043600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr8:59037200-59049200	Weak transcription	Brain Substantia Nigra	brain
20	chr8:59040200-59044000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr8:59040800-59044000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:59040800-59045200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr8:59041000-59044800	Weak transcription	Psoas Muscle	Psoas
24	chr8:59041200-59043800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr8:59041200-59044000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:59041200-59044000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:59041200-59044400	Enhancers	HMEC	breast
28	chr8:59041400-59044000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:59041400-59044200	Enhancers	NHEK	skin
30	chr8:59041400-59044400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:59041400-59048200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr8:59041800-59043600	Enhancers	Left Ventricle	heart
33	chr8:59041800-59044000	Enhancers	HSMM	muscle
34	chr8:59041800-59058000	Weak transcription	Colon Smooth Muscle	Colon
35	chr8:59042000-59043600	Enhancers	Right Atrium	heart
36	chr8:59042000-59043800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr8:59042000-59044000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr8:59042000-59044000	Enhancers	Placenta	Placenta
39	chr8:59042000-59044800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr8:59042000-59045000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr8:59042200-59044000	Enhancers	NHDF-Ad	bronchial
42	chr8:59042200-59044600	Enhancers	Gastric	stomach
43	chr8:59042200-59050200	Weak transcription	Lung	lung
44	chr8:59042400-59044800	Strong transcription	Fetal Muscle Leg	muscle
45	chr8:59042800-59043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:59042800-59043600	Enhancers	Osteobl	bone
47	chr8:59042800-59043800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr8:59042800-59044000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:59042800-59044600	Enhancers	HepG2	liver
50	chr8:59043000-59043600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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